PEAR - Paired-End reAd mergeR

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.

Latest News

PEAR 0.9.4 released

2014-08-08

An updated version of PEAR is released.

  • Support for bzip2 compressed files
  • Simplified code
  • Correct representation of degenerate characters on output (reverseded+complimented)

PEAR 0.9.3 released

2014-06-19

An updated version of PEAR is released.

  • Corrections in documentation
  • Added forgotten -c option in getopt_long (fix for capping quality scores in output)

PEAR 0.9.2 released

2014-03-31

An updated version of PEAR is released.

  • Added checks whether output files are writable
  • Fixed condition to allow 1 base long reads

PEAR 0.9.1 released

2014-01-31

An updated version of PEAR is released.

  • Capped the quality scores of the overlapping region
  • Minor bug fixes

PEAR 0.9 released

2013-11-20

An updated version of PEAR is released.

  • PEAR can now process paired-end reads where the lengths of the two ends differ
  • Added some statistics at output

PEAR 0.8.1 released

2013-07-19

An updated version of PEAR is released.

  • Fixed numerical issue when computing empirical base frequencies
  • Added a warning when input files differ in number of lines

PEAR Manual released

2013-06-19

A basic version of the PEAR manual was added to the website.

Version 0.8 released

2013-06-18

The first version of PEAR is finally available. It is available as a standalone library and in source code format.

  • Added memory options
  • Improved explanations in command-line arguments
  • Fixed usage of PHRED base

Important notice

The PEAR creative commons license prohibits commercial use of the code. For testing and using PEAR on a commercial basis you need to purchase a commercial software license. If you wish to purchase such a license please contact:
Prof. Alexandros Stamatakis

32-bit precompiled binary (i386)

pear-0.9.4-bin-32.tar.gz v0.9.4

64-bit precompiled library (x86_64)

pear-0.9.4-bin-64.tar.gz v0.9.4

Source code

pear-0.9.4-src.tar.gz v0.9.4